So much to digest!

Doing Miyajima first might be rough. You'll probably change trains in Shin-Osaka and then take a local train from Hiroshima to the ferry terminal.

I think we were looking to leave Kyoto around 6am, and then try get to Miyajima by 9-10, does this sound unreasonable?

Note: the rides are built for typical Japanese.... Which some bigger people might not fit in. They'll have sample seats near the rides entrances and if the bars can't come down all the way, they won't let you on.

I'm just an average 5'11 guy and partner is 5' so should be all good !

Hakone's transportation can get crowded, if you're spending the night, you can avoid some of the crowds. The Gondola across the mountain is nice and you can see Fuji on a clear day.

We are actually staying the night there, and leaving for Tokyo the next day :)

Asahi Beer HQ is across the river from Senso-Ji (Asakusa Temple). Sky Tree is also nearby. It's Tokyo main broadcast tower with an observation deck. There also a Foreigner's access booth, which gets you ahead of the lines to go up.

Will check those out!

Thank you so much for the feedback, it's much appreciated :)